+Open data
-Basic information
Entry | Database: PDB / ID: 3iql | ||||||
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Title | Crystal structure of the rat endophilin-A1 SH3 domain | ||||||
Components | Endophilin-A1 | ||||||
Keywords | PROTEIN BINDING / SH3 / endophilin / Coiled coil / Cytoplasm / Endocytosis / Lipid-binding / Membrane / Phosphoprotein / SH3 domain | ||||||
Function / homology | Function and homology information Negative regulation of MET activity / membrane bending / positive regulation of membrane tubulation / EGFR downregulation / lipid tube assembly / vesicle scission / membrane tubulation / basal dendrite / regulation of clathrin-dependent endocytosis / Retrograde neurotrophin signalling ...Negative regulation of MET activity / membrane bending / positive regulation of membrane tubulation / EGFR downregulation / lipid tube assembly / vesicle scission / membrane tubulation / basal dendrite / regulation of clathrin-dependent endocytosis / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / regulation of receptor internalization / negative regulation of blood-brain barrier permeability / synaptic vesicle uncoating / Golgi Associated Vesicle Biogenesis / dendrite extension / MHC class II antigen presentation / postsynaptic actin cytoskeleton organization / Recycling pathway of L1 / photoreceptor ribbon synapse / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynaptic cytosol / synaptic vesicle endocytosis / cellular response to brain-derived neurotrophic factor stimulus / hippocampal mossy fiber to CA3 synapse / negative regulation of protein phosphorylation / Schaffer collateral - CA1 synapse / synaptic vesicle membrane / neuron projection development / presynapse / postsynapse / transmembrane transporter binding / early endosome / negative regulation of gene expression / neuronal cell body / glutamatergic synapse / lipid binding / synapse / protein kinase binding / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Trempe, J.F. / Kozlov, G. / Camacho, E.M. / Gehring, K. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination. Authors: Trempe, J.F. / Chen, C.X. / Grenier, K. / Camacho, E.M. / Kozlov, G. / McPherson, P.S. / Gehring, K. / Fon, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iql.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iql.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 3iql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/3iql ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iql | HTTPS FTP |
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-Related structure data
Related structure data | 2knbC 1gcqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7981.790 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sh3d2a, Sh3gl2, Sh3p4 / Plasmid: pGEX-2TK / Production host: Escherichia coli (E. coli) / Strain (production host): K12 BL21 DE3 / References: UniProt: O35179 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 20% methyl-2,4-pentanediol, 0.1M sodium acetate, 0.05M calcium chloride, 10mM 2-mercaptoethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9772 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 2, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9772 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 24510 / Num. obs: 23667 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 11.1 / Num. unique all: 4701 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1GCQ, chain A, Non-conserved residue pruned to CB atom using CHAINSAW Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.467 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.739 Å2
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Refine analyze | Luzzati coordinate error obs: 0.151 Å / Luzzati d res low obs: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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